I am new to the genomics field and I have recently started working with SAMTOOLS. My question is the following:
- I have my SAM file with 2,5 M aligned reads.
- I convert it to BAM file with SAMTOOLS
- I make the index of the BAM and the reference file
What I want to do is use the tview command to study a region of interest (say position 150-160). So I write this:
samtools tview -d T -p ref_cons:145 BAM_FILE --reference REFERENCE_FILE
It works fine, BUT the problem is that it returns only ~8,000 lines (reads). My question then is if there is some limit of the number of alignments that are outputted and, if so, how can I make it so that it prints all of them? I attach a screen-shot of the output I am getting.